Related papers: Checking Phylogenetic Decisiveness in Theory and i…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
A key question in biological systems is whether genetic diversity persists in the long run under evolutionary competition or whether a single dominant genotype emerges. Classic work by Kalmus in 1945 has established that even in simple…
Our goal in this paper is to automatically extract a set of decision rules (rule set) that best explains a classification data set. First, a large set of decision rules is extracted from a set of decision trees trained on the data set. The…
Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
The input to the no-rainbow hypergraph coloring problem is a hypergraph $H$ where every hyperedge has $r$ nodes. The question is whether there exists an $r$-coloring of the nodes of $H$ such that all $r$ colors are used and there is no…
Complex classifiers may exhibit "embarassing" failures in cases where humans can easily provide a justified classification. Avoiding such failures is obviously of key importance. In this work, we focus on one such setting, where a label is…
We prove that a wide range of coloring problems in graphs on surfaces can be resolved by inspecting a finite number of configurations.
It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…
We study the fundamental question of how informative a dataset is for solving a given decision-making task. In our setting, the dataset provides partial information about unknown parameters that influence task outcomes. Focusing on linear…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
Program correctness (in imperative and functional programming) splits in logic programming into correctness and completeness. Completeness means that a program produces all the answers required by its specification. Little work has been…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
This paper categorizes the parameterized complexity of the algorithmic problems Perfect Phylogeny and Triangulating Colored Graphs when parameterized by the number of genes and colors, respectively. We show that they are complete for the…
We study the problem of determining what data is required to solve a decision-making task when only partial information about the state of the world is available. Focusing on linear programs, we introduce a decision-focused notion of data…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
A default theory can be characterized by its sets of plausible conclusions, called its extensions. But, due to the theoretical complexity of Default Logic (Sigma_2p-complete), the problem of finding such an extension is very difficult if…
When modeling an application of practical relevance as an instance of a combinatorial problem X, we are often interested not merely in finding one optimal solution for that instance, but in finding a sufficiently diverse collection of good…
A graph is $\ell$-choosable if, for any choice of lists of $\ell$ colors for each vertex, there is a list coloring, which is a coloring where each vertex receives a color from its list. We study complexity issues of choosability of graphs…